The Crystal Origins
by rabidminimoose
Summary: Scarlett always wondered where her father found the crystal that allowed teleportation possible...Patrick is reluctant to tell her. He tells her he is ashamed at his failed promise to a dear friend that might have changed the very fate of the world. A story of the MASS crystal with a side of SE/TR with a hint of TR/oc.
1. Chapter 1

The Joes managed to infiltrate an abandoned Cobra facility in the desert to ensure all weapons and toxins are properly disposed of. The location was given by Scarlet's father rather reluctantly after Scarlet had asked him if there were any other facilities of cobra that they need to know of. Snake Eyes was situated outside to patrol the vicinity when he was surprised by an arrow, it had almost hit his neck had he not turned at that moment. The ninja flipped backwards, running towards the entrance to the facility bright feathered arrows trailing behind him as they missed their target. He heard an elk call that he guessed was really his enemy. Snake Eyes paused and he could make out a hazy distorted image of a man, the distortion brought on from the heat of the desert sand. The male had a buffalo crown head piece with white war paint, leather vest with leather chaps over jeans. Snake Eyes drew his katanas and waited as the other approached.

"You there! Why have you come to this place?" Snake Eyes was caught off guard by the question considering he had no way of answering. He touched his throat and shook his head to try to convey his disability.

"Ah like the Great Wanderer you are silent but I can tell you long to speak. I must warn you of this place my fellow brother. This place was abandoned long ago. Even though Cobra tried to reopen this facility, the Great Spirits have forbid any acts of opening the door to the Spirit World. I had thought you were an enemy of the spirits as I would like to think of myself as a spirit protector. The Wanderer incarnate gave that man her key in order to help mankind. She was greatly disappointed and she fled from this place." The man showed his bow and arrows and placed them on the ground.

"I have need of you to find this Wanderer incarnate. I have relayed to you the story the nearby tribe had told me. I am from the sioux tribe and I have need to call upon the Great Wanderer so that my tribe may once again be at peace with the great spirits." The man sighed. "It has been a long journey. Come I may be able to decipher the information you may find in this facility." The man motioned for Snake Eyes to respond. Snake Eyes was intrigued by this story. He knew that Scarlett's father had obtained the crystal by some means but to think that he obtained it from an indigenous tribe? Did they once have such technology in the past to activate the stone?

"The Crystal was the Wanderer Incarnate's key to the Spirit world. Only she and the Spirits have knowledge on how to open the 'Door'." The man sighed waiting on Snake Eyes to make his move. Just then the facility's entrance doors opened to reveal Duke, plasma pistol at the ready.

"You O.K Snake Eyes?" Duke kept his eyes on the new comer and walked closer to the two.

"I mean you no harm. Please, I require your help. I need to find out what happened to the Wanderer Incarnate and where she could possibly be. I thank you for infiltrating the facility, I had expected it to be difficult to open." Spirit smiled nervously and waited for the newcomer to allow him to move freely.

"Uh...ok then. Um...and you are?" Duke was confused not like it was any different when dealing with snake eyes.

"You may call me Spirit Talmos. I am part of the Sioux Tribe and I seek information inside that facility." Spirit dropped his hands as his muscles ached from readying all those arrows.

Duke was still suspicious but he wanted the others' opinions before he started playing cop again. He radioed the others to come outside, Scarlet outright refusing while the others quickly ran to Duke's side. Duke was annoyed at Scarlet, she seemed like she was once again obsessed with cobra or rather the information that cobra had been hiding.

"What's the matter Duke?" Roadblock said staring at the stranger. The man was tall and wore very 'unique' clothing styles. 'I don't like the looks of this.' Roadblock straighten himself to make him appear taller so as to intimidate the stranger.

"This guy says he needs some information from the facility. Says he is from a sioux tribe?" Duke could tell the man was a native american but he wasn't very knowledgeable about specific tribes. "Anyways, he attacked snake eyes and now he wants peace. Any objections?" Duke asked.

"Was the ninja hurt?" Tunnel rat asked squinting from the harsh light of the afternoon sun. He hated deserts and wanted to stay at the base but Duke ordered him to go as he was the only medic Duke trusts.

"See for yourself T-rat." Ripcord pointed to the silent man and Tunnel Rat sighed in annoyance at his nickname.

"The name i-" Tunnel Rat was interrupted by a staticky message from Scarlett.

"Everyone should come and see this. The new comer too."

"This just keeps getting better and better." Duke groaned and then motioned for all the others to head inside. He waited for Spirit to grab his fallen weapons and join them.

"Thank you." Spirit said passing Duke.

"We haven't done anything." Duke shook off the thanks and made his was to the elevator.

When the group reached the level they had left Scarlett they were surprised to see holograms of various crystals throughout the laboratory. Scarlett waved for them to come closer.

"I think I found some history on the crystal that allowed teleportation. It's a rare crystal that was noted by various historical journals but there were never any specimens. Until some how my father managed to get his hands on one. I think I need to talk to h-"

"By the maker that is the crystal of the Wanderer. How...do you know of this stone? I demand you tell me right now!" Spirit was angry that his race's most treasured artifact, the stone that once brought together every tribe to overcome a great strife had fallen into an outsider's hand.

"I wouldn't do that buffalo man." Ripcord readied to activate his alternate form. Duke had his plasma pistol at the ready.

"How do you know of the crystal? Cobra kept this information locked tight. Wait...it was a native american artifact?" Scarlett was awestruck that the indigenous held such a powerful stone.

"Yes, the stone was used to open the gates of the spirit realm. Only the chosen Wanderer who held within their soul a fragment of the original Wanderer could use the stone's power. I believe the current Wanderer incarnate was held here and something went wrong. I need to find out whether she is alive or not so I might find away to calm my land's spiritual balance. If not, my tribe will be cursed until there is no trace of our lineage." Spirit clenched his hands in agitation. 'Why can't they see?'

Suddenly a new hologram popped up infront of Scarlett. It was a video file and if a nervous look to Spirit, Scarlett touched the file in order for it to play. Scarlett gasped as she saw her mother and father. They were talking with a young woman who seemed to be extremely happy. Her mother hugged the woman and looked toward the camera.

"This will mark the first day of your new life Madja. We'll help you get through this...together." Scarlett's mother smiled so bright and her father laughed as the woman bowed in thanks.

"Madja...let's go to the lab for some tests." Scarlett's father walked out of the frame and the woman soon followed. Her mother looked to the video and said.

"Today an Algonquin shaman has agreed to teach us their mysterious healing. Come on DeCobray lets go to the lab." the video ended and an electronic text moved across the room, end of journal entry zero zero five. Scarlett was left speechless for she had no idea her mother was also involved in Cobra.

"Madja...the young woman heard the Wanderer's voice and so she became the incarnate. However she was a fraternal twin and this has never happened in all passed down history. It was unfortunate but one had to be...removed." Spirit started to explain the woman's history rather abruptly and Scarlett shook her head in denial that her entire family was a part of Cobra.

"Spirit I don't think we need to kno-" Duke was cut off by a sudden radio message.

"Scarlett? This is your father, I just received a beacon of your location within my mobile device. I placed this beacon to alert me of anyone trying to delve into information that I promised would stay hidden. I would appreciate you keep whatever you found to yourselves and return to base immediately." Dr. O'hara sounded perturbed and when the radio clicked off.

"You heard him Duke. Let's move out." Scarlett headed over to the elevator her face expressionless.

"Wait Scarlett!" Duke hurried to her side. The others followed confused about what just transpired. Spirit hesitated and then joined the joes in the elevator.

"I wish to meet your father. If he knows anything about what happened to Madja." Spirit pleaded with Scarlett.

"You can come but...let me speak to him first. I have some questions of my own." Scarlett became silent and withdrawn the entire journey back to base. The others were starting to worry.

A/N: sorry for no update for so long. Anyways...madja is the algonquin word for hear. It is the her name the shaman granted her. Her real name is yet unknown for true names are kept secret in many tribes. What will Patrick O'Hara reveal to the Joes.


	2. Chapter 2

When the Joes arrived at base they were immediately confronted by the colonel and Patrick O'Hara. They all made there way inside to the control room when Scarlett attacked her father with accusations. Patrick allowed his daughter to finish and then eventually told them everything he know about Cobra.

Scarlett stood before her father with anger and disbelief across her face. The whole team were introduced to more of the atrocities Cobra committed. Not only had Cobra managed to capture a very important piece of indigenous history, they eliminated the entire tribe and any evidence of its existence. Dr DeCobray had various government contacts that allowed that to happen and after the professor revealed what happened the colonel shook his head in disgust and left to contact the various government agencies in order to rectify the mistake.

"And there were no survivors of the massacre? Father...h-" Scarlett got interrupted by her father.

"There was only one survivor and she was held for experimentation. She lived for five years without knowing about what had transpired. She wrote to her family and friends and we kept those letters, hell, we would even forge responses. Madja she...I would feel so disgusted with myself and then one day she." Patrick became emotional as he remembered his dear friend the day he revealed what Cobra had done. That day Patrick knew she died and her eyes showed that. "I told her everything and Madja became withdrawn and eventually catatonic . She would remain unresponsive even when Dr. DeCobray...that bastard injected her with a new drug. Her screams of agony reached my lab and as I tried to open the lab doors I saw your mother, Lakota. She apparently tried to prevent DeCobray from his cruelty and paid it with her life. As I saw both my love and my dear friend in that lab I knew that I had to get out before that madman got to you. DeCobray hadn't seen me and I secretly planned a way to eventually cut my ties with everything Cobra. It would have also freed Madja but then as the drug caused her nerve endings to fry, she was left with almost no feeling in her entire body. She could only sense pressure, pain had no effect and DeCobray used that as a way to skip preparing anesthesia for her various 'Surgeries' that he said would help correct it. I was the only one to know that it was all a lie. DeCobray didn't count on the fact that she was also planning her own escape and I witnessed the death of the then head of Cobra Industries, Adam's father as Madja used the stone to crumple the labs. She managed to gain strength as the stone shattered and some of the pieces were absorbed in her body. Madja...she wasn't herself anymore." Patrick wished he managed to gain those data logs of the attack.

"It was the wanderer that helped his incarnate gain her freedom." Spirit closed his eyes in reverence.

"The wanderer? Who and what is this wanderer I heard Madja talking about it with Lakota." Patrick had often wondered what the two women in his life would talk about almost everyday. Lakota had been a researcher into indigenous people and desired to gain as much knowledge from the people as she could. She was only at the Cobra labs because she begged him to allow her to remain at Madja's side. DeCobray allowed it so long as Lakota not be a bother to the other researchers. 'If only I said no.' Patrick regretted allowing his love to be at the labs.

"Yes, it is a deity figure that is said to have united all the people of the world to overcome a great evil. It is said the stone the wanderer held in his power had shattered, the pieces finding themselves within his incarnations. The stone that Madja held shattered again?" Spirit was surprised the stone would do such a thing.

"Yes, it appeared that the ones that embedded themselves into her body gave Madja inhuman strength. She seemed to go beserk and completely destroyed the lab she was held within until she eventually broke through to the surface. I witnessed her escape and the roar that she let out at her freedom would forever haunt me...I am sure it haunted Adam or should I call the bastard Cobra Commander?" Patrick spat at the nickname of his once close associate.

"I see. So you do not know the whereabouts of the woman do you?" Spirit turned as if he was leaving before he was stopped by Patick.

"What do you want with her if I did know her location?" Patrick questioned the new comer. He could tell he was indigenous and he was afraid of what the man would want with Madja.

"She was the rightful incarnate and so she holds responsibilities that she must uphold." Spirit turned with a sharp look to Patrick.

"Her tribe forced her to kill her own twin brother. I don't think she needs to fulfill anymore 'responsibilities' like that." Patrick and Spirit stared each other down. The rest of the joes were all confused about what the two were talking about.

"Never has the incarnation became two beings. It was always one and her tribe did the right thing. By removing the other and obtaining the stone of her brother Madja had a better connection with the Wanderer. She gained so much from her brother's deat-"

"Her brother was her only family that she knew of. She had been abandoned by her mother and the tribe took the two in and cared for them. She loved her brother and to have to take his life in order to remain a part of the tribe...or to even exist as the Shaman told her. It was too much. This wanderer incarnate thing, she told me she didn't believe she was so special and denied her namesake. Madja told me she kept the name the shaman gave her to remind herself to always hear her brother's cries of sorrow. She threw away her responsibilities and allowed us to take the stone. The stone was nothing special or rather we couldn't activate the damn thing. Adam's father became furious and eventually gave up, allowing Adam to start his experimentation with Madja. This Wanderer stuff is old myths and nothing more so lets just leave her alone." Patrick was growing furious with Spirit.

"You witnessed the stone's power when held within Madja's hands and yet you deny she is any special from other people." Spirit shook his head.

"That is why...I...that is why I created the M.A.S.S device. Madja came to me one year after her escape in secret. She knew I had collected the two shards that had failed to converge with her body. She told me what I needed to activate the stone. And then the day came where Adam found out what I was doing." Patrick tightened his fists in rage.

"Dad...Cobra Commander is dead now." Scarlett was at a loss of words on how to comfort her father. It was obvious this made him distressed.

"I know but I still wished I was there to finish that bastard off." Patrick closed his eyes and let out a sigh. "Fine stranger. I'll tell you where you may find Madja but you must be accompanied by Shana and her team. Shana...I need to ask you a favor. I promised Madja I would bring back her brother's stone. And what happened to both shards...I can't really face Madja right now can I?" Patrick looked away in shame.

"Come on Father don't be a coward." Scarlett glared at her father for his cowardice.

"I don't even know if she is still at that location." Patrick sighed.

"Then we will investigate and if she is there...I'll radio you the coordinates and then you can tell her yourself."

"Fair enough Shana...her last location was in South Dakota. The last message came from the town of Custer. Good luck all of you." Patrick sat down and held his head in his hands.

Shana didn't want to further disturb her father so she silently nodded to the others to move out. The team decided to take the Coyote again and prepared for the worst. Tunnel Rat was excited for he knew about the Jewel Caves and secretly packed his sewer diving gear. He wanted to explore the real underground and he daydreamed what all the treasure he could find. The others didn't share the same excitement and Spirit remained almost as silent as the ninja through out the trip.

A/N Madja was greatly weakened for using her brother's stone...so don't think is the overpowered mary sue...I hate those. Some new characters to enter as well...hopefully you guys enjoy them. lol update...um I don't know my cities...BAHAHAH anyways...yeah. MY BAD GUYS LOL I AM WRITING THE THIRD CHAPTER! thanksgiving has been nothing but food and boredom...


	3. Chapter 3

Inside a decrepit building Cobra Commander surveys the area. Zartan stood a few feet away with his arms crossed, smirking at the once powerful commander.

"So what will it be my dear Cobra commander?" Zartan asked the other, he knew he already won and that the Commander would be at his beck and call. The commander had gained some serious damage after the Joes had destroyed his base and it was Zartan that found him. Cobra Commander owed him so much Zartan smiled at his future plans. The other man walked stiffly away his breathing laborious.

"I will be your pawn but I ask of you to do me just one more favor." Cobra Commander coughed and waited for Zartan's reply.

"Sure thing Commander what is this little favor?" Zartan was sure it was a small useless favor that he could get done easily.

"I want to know the whereabouts of a certain person. Can you find this out, Zartan?" Cobra Commander turned to the hooded Chameleon.

"Heh...that all ya want? Sure it won't take me long. Tell me the name of this person and we can start." Zartan waited for the commander to give him information.

"A woman that was once named Madja. I need to know where she might be." Coughing once more Cobra Commander leaned against the wall as his strength started to wane. "Find her and I will do what ever you want Zartan." He sat on the ground closing his eyes as Zartan approached him.

"Fine, I will find this woman for ya. Stay with my gang and restore your strength I need you to be alive when I came back." Zartan left to find his close contact that has a way with finding out about people. 'Piece of cake.'

* * *

The ride to South Dakota was a boring one and Nicky felt like he wanted to jump out of the car from Roadblock's singing. The others were more subtle about their annoyances but Nicky wasn't having it.

"EH! You can't sing Roadblock so STOP IT PLEASE FOR THE LOVE OF GOD!" Tunnelrat wanted to punch the seat in front of him that roadblock was sitting in. He knew better than to mess with the big guy physically though.

"Well I guess since you said please." Grumbled Roadblock as he turned off his music, he was getting bored of it anyways.

As the Coyote sped on, Duke saw the welcome sign of the city.

"Well there's Custer. So her location would be on the west side of the city. Should we stop for some questioning?" Duke really wanted to stop but he asked their 'leader' on what to do.

"Sure, I could use some fresh air anyways." Scarlett sighed and resumed looking out the window. Almost everyone smiled as Scarlett agreed with Duke, excited to get out of the vehicle.

"Wait...stop the car please." Spirit stood up and grabbed the top of Duke's seat. Duke glared at Spirit for a second before he drove to the side of the road and stopped.

"What is it Spirit?" Duke asked seriously wanting to reach the city before dark.

"I sense...I sense something." Spirit walked out and looked on to the mountainous area covered in green forests. Duke unbuckled himself and also got out of the vehicle.

"Ripcord? Do you sense something too?" Duke asked Weemes.

"No...wait." Ripcord closed his eyes as he felt something.

"It's the spirit world...someone has opened a path." Spirit ran off into the forest and Duke yelled and gave chase.

Scarlett looked on and sighed. 'at this rate we won't find Madja.' She got out followed by tunnel rat, roadblock, and snake eyes. She surveyed the forest before she gave Snake eyes a nod. The ninja nodded back and ran after the other two.  
"Well what do we do then Red?" Tunnel rat asked miffed at the situation.

"Well what can we do?" Scarlett directed it to herself than to the others.

Suddenly a whistle was sounded that pierced through the forest. The three prepared for a possible attack. Out of the forest walked a young male that looked at the three in curiosity.

"Why is a kid out in the middle of no where?" Nicky asked aloud and relaxed his stance.

"Don't lower your guard so soon private!" Scarlett yelled back unsure if this could be a trap.

"Whoa whoa! Quiet you crazy adults! Otherwise you might attract them to this place." The kid placed his index finger to his lips and smiled, winking at Scarlett. She glared but said nothing.

"Who are 'they' and are they dangerous?" Tunnelrat went straight to the point and wanting to know if there was a threat.

"Well...you could say they're dangerous. Only to those that are bad though or so that's how the legend goes." The kid talked very quietly and the three strained to hear him.

"Wait...is this just folk lore you're talking about?" Roadblock let his guard down while he talked and that was when he felt a sting in his neck. His vision was edged in shadow as he tried to warn the others but he saw that they too were in the same state as he. 'Guess Scarlett was right...again.' Roadblock and the others fell to the ground unconscious.

"You know you could have been more gentle with the red head." The teen asked aloud as a cloaked figured stood atop the Coyote.

"Aww...someone has a crush. Now is not the time, a spirit guardian has sensed the opened path. We need to stop them before they reach the cave. Tie these three up and meet me at the cave entrance Hawke" The cloaked figured then disappeared in a bright blue flash.

"Yeah yeah. Great that big one is gonna be a pain in the ass to move." Hawke was not looking forward to his new mission.

* * *

Duke cursed as he was cut from the pine branches, Spirit was making it difficult to catch up to.

"Spirit! Stop!" Duke yelled hoping Spirit would actually stop. 'Or just slow the fuck down so I can catch up and punch you.' Duke growled in frustration as another branch smacked him in the face while he wasn't paying attention. Duke suddenly saw a shadowy figure out the corner of his vision, Duke turned his head to see the ninja.

"Snake Eyes! Can you catch up to Spirit? I-gruh" Duke smacked into a trunk of a pine and fell. The ninja was soon by his side.

"I'm fine...just go and catch Spirit." Snake Eyes nodded and then was off. "The next time I see Spirit...I'm gonna ouch!" As soon as Duke stood up there was a sudden pain in his neck. Duke felt the back of his neck and pulled out the dart. 'What the hell is...is' Duke soon lost his balance and fell, staring up he noticed a masked face looking down at him then only darkness.

* * *

A/N...Omg I am so excited for where I am trying to get to...yeah...someone opened a path to the spirit world...bad because demons and other spirits now have a chance at gaining a physical form. The Wanderer was the one that managed to lock the evil and the dead to remain separate from the living and physical. The stone holds the power to distort reality thus allowing teleportation as well as other features. What has become of Madja and who are these people that so far got most of the Joes. Will Snake Eyes be able to catch Spirit? lol I am typing it as I post this so stay tuned!


End file.
